加载中…科技日报--细菌酶（下）
(2022-06-05 13:02:44)
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科技日报细菌酶杂谈 |
分类： 翻译 |
A close-up look at Kitasatospora setae, a bacterium isolated from soil in Japan. These bacteria fix carbon – turn carbon dioxide from their environment into biomolecules they need to survive – thanks to enzymes called ECRs. Researchers are looking for ways to harness and improve ECRs for artificial photosynthesis to produce fuels, antibiotics and other products. Credit: Y. Takahashi & Y. Iwai, atlas.actino.jp
近距离观察从日本土壤中分离出的一种细菌 Kitasatospora setae。 这些细菌可以固定碳，即将环境中的二氧化碳转化为它们生存所需的生物分子，这要归功于称为 ECR 的酶。 研究人员正在寻找利用和改进用于人工光合作用的 ECR 以生产燃料、抗生素和其他产品的方法。 图片来源：Y. Takahashi 和 Y. Iwai，atlas.actino.jp
What’s more, he said, the step in natural photosynthesis that fixes CO2 from the air, which relies on an enzyme called Rubisco, is a bottleneck that bogs the whole chain of photosynthetic reactions down. So using speedy ECR enzymes to carry out this step, and engineering them to go even faster, could bring a big boost in efficiency.
此外，更重要的是，他说，在自然光合作用中，光合作用从空气中固定二氧化碳的步骤依赖于一种叫做Rubisco的酶， 它是阻碍整个光合反应链的瓶颈。因此，使用快速 ECR 酶来执行这一步骤，并将它们设计得更快，可以大大提高效率。
We aren’t trying to make a carbon copy of photosynthesis,” Erb explained. “We want to design a process that’s much more efficient by using our understanding of engineering to rebuild the concepts of nature. This ‘photosynthesis 2.0’ could take place in living or synthetic systems such as artificial chloroplasts – droplets of water suspended in oil.”
“我们并不是想复制光合作用的副本，”Erb 解释说。 “我们希望通过利用我们对工程的理解来重建自然概念，来设计一个更高效的流程。 这种‘光合作用 2.0’可以发生在活体或合成系统中，例如人造叶绿体——悬浮在油中的水滴。”
Portraits of an enzyme
Wakatsuki and his group had been investigating a related system, nitrogen fixation, which converts nitrogen gas from the atmosphere into compounds that living things need. Intrigued by the question of why ECR enzymes were so fast, he started collaborating with Erb’s group to find answers.
酶的肖像
Wakatsuki 和他的团队一直在研究一个相关的系统，即固氮，该系统将大气中的氮气转化为生物所需的化合物。Wakatsuki对ECR 酶为何如此之快的问题很感兴趣，他开始与 Erb 的小组合作以寻找答案。
Hasan DeMirci, a research associate in Wakatsuki’s group who is now an assistant professor at Koc University and investigator with the Stanford PULSE Institute, led the effort at SLAC with help from half a dozen SLAC summer interns he supervised. “We train six or seven of them every year, and they were fearless,” he said. “They came with open minds, ready to learn, and they did amazing things.”
Hasan DeMirci 是 Wakatsuki 小组的一名研究助理，现在是 Koc 大学的助理教授，也是斯坦福 PULSE 研究所的研究员，在他指导的六名 SLAC 暑期实习生的帮助下，领导了 SLAC 的工作。“我们每年培训六七个人，他们无所畏惧，”他说。 “他们怀着开放的心态，准备好学习，他们做了令人惊奇的事情。”
The
SLAC team made samples of the ECR enzyme and crystallized them for
examination with X-rays at the
SLAC 团队制作了 ECR 酶样本，并将其结晶，以便在美国能源部阿贡国家实验室的高级光子源进行 X 射线检查。 X 射线揭示了这种酶的分子结构：无论是单独存在还是附着在促进其工作的小辅助分子上时的原子支架排列。
Further X-ray studies at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) showed how the enzyme’s structure shifted when it attached to a substrate, a kind of molecular workbench that assembles ingredients for the carbon fixing reaction and spurs the reaction along.
在 SLAC 的斯坦福同步辐射光源 (SSRL) 进行的进一步 X 射线研究表明，当酶附着在底物上时其结构发生的变化，底物是一种为碳固定反应组装成分并促进反应的分子工作台。
ECR是一种在土壤细菌中发现的一种酶，这种描述显示其四种相同的分子具有不同的颜色。这些分子成对地一起工作——蓝色与白色，绿色与橙色——将微生物环境中的二氧化碳转化为其生存所需的生物分子。一项新的研究表明，少量分子胶、及时的摆动和扭曲可以使这些对同步运动，比植物酶在光合作用中快20倍固定碳。图片来源：H.DeMirci等人，ACS中心科学，2022年
Finally, a team of researchers from SLAC’s Linac Coherent Light Source (LCLS) carried out more detailed studies of the enzyme and its substrate at Japan’s SACLA X-ray free-electron laser. The choice of an X-ray laser was important because it allowed them to study the enzyme’s behavior at room temperature – closer to its natural environment – with almost no radiation damage.
最后，来自 SLAC 直线加速器相干光源 (LCLS) 的一组研究人员在日本 SACLA X 射线自由电子激光器上对酶及其底物进行了更详细的研究。 X 射线激光器的选择很重要，因为它使他们能够研究酶在室温（更接近其自然环境）下的行为，几乎没有辐射损伤。
Meanwhile, Erb’s group in Germany and Associate Professor Esteban Vo¨hringer-Martinez’s group at the University of Concepción in Chile carried out detailed biochemical studies and extensive dynamic simulations to make sense of the structural data collected by Wakatsuki and his team.
与此同时，德国的 Erb 小组和智利康塞普西翁大学的 Esteban Vo¨hringer-Martinez 副教授小组进行了详细的生化研究和广泛的动态模拟，以了解 Wakatsuki 及其团队收集的结构数据。
The simulations revealed that the opening and closing of the enzyme’s two parts don’t just involve molecular glue, but also twisting motions around the central axis of each enzyme pair, Wakatsuki said.
Wakatsuki 说，模拟显示，酶的两个部分的打开和关闭不仅涉及分子胶，还涉及围绕每个酶对的中心轴的扭转运动。
“This twist is almost like a rachet that can push a finished product out or pull a new set of ingredients into the pocket where the reaction takes place,” he said. Together, the twisting and synchronization of the enzyme pairs allow them to fix carbon 100 times a second.
“这种扭曲几乎就像一个棘轮，可以将成品推出或将一组新成分拉入发生反应的口袋中，”他说。 总之，酶对的扭曲和同步使它们能够每秒固定碳 100 次。
The ECR enzyme family also includes a more versatile branch that can interact with many different kinds of biomolecules to produce a variety of products. But since they aren’t held together by molecular glue, they can’t coordinate their movements and therefore operate much more slowly.
ECR 酶家族还包括一个更通用的分支族，可以与许多不同种类的生物分子相互作用以生产各种产品。但由于它们不是通过分子胶粘在一起的，无法协调它们的运动，因此运行速度要慢得多。
“If we can increase the rate of those sophisticated reactions to make new biomolecules,” Wakatsuki said, “that would be a significant jump in the field.”
“如果我们能够提高这些复杂反应的速度以制造新的生物分子，”Wakatsuki 说，“那将是该领域的一次重大飞跃。”
From static shots to fluid movies
So far the experiments have produced static snapshots of the enzyme, the reaction ingredients and the final products in various configurations.
“Our dream experiment,” Wakatsuki said, “would be to combine all the ingredients as they flow into the path of the X-ray laser beam so we could watch the reaction take place in real time.”
从静态镜头到流动电影
到目前为止，实验已经产生了酶、反应成分和各种配置的最终产品之静态快照。
“我们的梦想实验，”Wakatsuki 说，“是当所有成分流入 X 射线激光束的路径时结合所有成分，这样我们就可以实时观察反应的发生。”
The team actually tried that at SACLA, he said, but it didn’t work. “The CO2 molecules are really small, and they move so fast that it’s hard to catch the moment when they attach to the substrate,” he said. “Plus the X-ray laser beam is so strong that we couldn’t keep the ingredients in it long enough for the reaction to take place. When we pressed hard to do this, we managed to break the crystals.”
他说，实际上团队在 SACLA 尝试过，但没有奏效。 “二氧化碳分子非常小，它们移动得如此之快，以至于很难捕捉到它们附着在基材上的那一刻，”他说。 “此外，X 射线激光束非常强大，以至于我们无法将成分保留在其中足够长的时间以发生反应。 当我们努力做到这一点时，我们设法打破了晶体。”
An upcoming high-energy upgrade to LCLS will likely solve that problem, he added, with pulses that arrive much more frequently – a million times per second – and can be individually adjusted to the ideal strength for each sample.
他补充说，即将到来的对 LCLS 的高能升级可能会解决这个问题，脉冲到达的频率要高得多，每秒一百万次，并且可以单独调整到每个样本的理想强度。
Wakatsuki said his team continues to collaborate with Erb’s group, and it’s working with the LCLS sample delivery group and with researchers at the SLAC-Stanford cryogenic electron microscopy (cryo-EM) facilities to find a way to make this approach work.
Wakatsuki 说，他的团队继续与 Erb 的小组合作，并且正在与 LCLS 样品交付小组以及 SLAC-Stanford 低温电子显微镜 (cryo-EM) 设施的研究人员合作，以找到使这种方法发挥作用的途径。
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